Contacts of the helix formed by residues 177 - 188 (chain J) in PDB entry 6H25
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 177 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175J THR* 3.4 14.1 + - - +
176J ASN* 1.3 77.4 - - - +
178J ARG* 1.3 73.1 + - - +
179J ARG* 3.1 28.0 + - - +
180J ASN* 3.2 31.9 + - - +
181J LYS 3.4 7.4 + - - -
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Residues in contact with ARG 178 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176J ASN 3.4 5.0 + - - +
177J ASP* 1.3 74.3 + - - +
179J ARG* 1.3 60.1 + - - +
181J LYS* 3.2 24.3 + - - +
182J GLU* 2.9 26.0 + - - +
193J THR* 4.9 7.2 - - + -
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Residues in contact with ARG 179 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177J ASP* 3.1 20.6 + - - +
178J ARG* 1.3 77.0 - - - +
180J ASN* 1.3 61.3 + - - +
182J GLU* 3.2 9.2 + - - +
183J LYS* 2.9 26.7 + - - +
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Residues in contact with ASN 180 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69J ASP* 4.5 10.5 + - - +
71J ASN* 5.9 2.6 - - - +
146J ASN* 5.2 12.1 + - - +
150J ARG* 5.4 4.9 + - - -
173J PHE* 5.2 6.1 - - + -
175J THR* 3.7 15.3 + - - +
177J ASP* 3.2 34.5 + - - +
179J ARG* 1.3 74.8 - - - +
181J LYS* 1.3 60.7 + - - +
183J LYS* 3.3 9.1 + - - +
184J ALA* 2.9 27.9 + - - +
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Residues in contact with LYS 181 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173J PHE* 5.8 0.7 - - - -
175J THR* 3.9 17.4 - - + +
177J ASP 3.4 2.8 + - - -
178J ARG* 3.2 20.1 + - - +
180J ASN* 1.3 79.5 - - - +
182J GLU* 1.3 56.0 + - - +
184J ALA* 3.3 6.4 + - - +
185J ILE* 2.9 50.5 + - + +
191J ALA* 3.9 21.1 - - + +
192J PHE* 3.8 31.2 - - - -
193J THR* 3.7 18.6 - - + +
196J GLU* 4.6 10.4 + - - +
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Residues in contact with GLU 182 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178J ARG 2.9 13.2 + - - +
179J ARG* 3.2 12.1 + - - +
181J LYS* 1.3 78.3 - - - +
183J LYS* 1.3 56.3 + - - +
185J ILE* 3.4 10.0 + - - +
186J GLU* 2.9 28.9 + - - +
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Residues in contact with LYS 183 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150J ARG* 3.9 24.5 - - - +
179J ARG 2.9 13.4 + - - +
180J ASN* 3.3 13.2 + - - +
182J GLU* 1.3 76.8 - - - +
184J ALA* 1.3 58.3 + - - +
186J GLU* 3.7 5.2 - - - +
187J GLU* 2.9 37.0 + - + +
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Residues in contact with ALA 184 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150J ARG* 5.0 12.1 - - + +
173J PHE* 4.5 9.0 - - + -
180J ASN 2.9 17.4 + - - +
181J LYS* 3.6 5.6 - - - +
183J LYS* 1.3 73.9 - - - +
185J ILE* 1.3 65.2 + - - +
187J GLU* 4.4 3.2 - - - +
188J GLY 3.1 17.8 + - - -
189J ILE* 3.0 39.1 + - + +
191J ALA* 4.2 15.0 - - + -
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Residues in contact with ILE 185 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181J LYS* 2.9 45.9 + - + +
182J GLU* 3.7 7.9 - - - +
183J LYS 3.3 0.2 - - - -
184J ALA* 1.3 77.1 - - - +
186J GLU* 1.3 62.4 + - - +
188J GLY 3.3 14.6 + - - +
189J ILE 3.8 12.3 - - - +
190J PRO* 5.2 2.2 - - + -
191J ALA 4.9 10.1 - - - +
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Residues in contact with GLU 186 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182J GLU 2.9 18.1 + - - +
183J LYS* 3.3 7.8 + - - +
185J ILE* 1.3 77.2 - - - +
187J GLU* 1.3 63.0 + - + +
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Residues in contact with GLU 187 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147J ARG* 5.4 5.6 - - - +
150J ARG* 3.2 56.0 + - - +
151J VAL* 5.8 2.1 - - - +
154J LYS* 4.2 20.0 + - + +
183J LYS* 2.9 18.9 + - + +
184J ALA* 4.4 3.4 - - - +
186J GLU* 1.3 80.2 - - + +
188J GLY* 1.3 58.6 + - - +
189J ILE* 6.5 0.2 - - + -
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Residues in contact with GLY 188 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154J LYS* 5.2 10.3 - - - -
157J ASN* 5.7 0.7 - - - -
184J ALA 3.1 8.5 + - - +
185J ILE* 3.3 14.0 + - - +
187J GLU* 1.3 81.0 - - - +
189J ILE* 1.3 66.6 + - - +
190J PRO* 4.7 0.3 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il